R/Bioconductor package for identification of triplex-forming sequences

Czech title

R/Bioconductor balíček pro identifikaci sekvencí tvořících triplex

Type

software

License

optional - free

Authors

Hon Jiří, Ing. (FIT BUT)
Lexa Matej, Ing., Ph.D. (FI MUNI)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Rajdl Kamil, Mgr. (FI MUNI)

Keywords

H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation

Description

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Location

http://www.bioconductor.org/packages/release/bioc/html/triplex.html

Licence

Free software under the terms of BSD license (see http://www.opensource.org/licenses/bsd-license.php).

Projects

Security-Oriented Research in Information Technology (MSM0021630528)
The IT4Innovations Centre of Excellence (ED1.1.00/02.0070)

Departments

Faculty of Informatics MU (FI MUNI)
Faculty of Information Technology BUT (FIT BUT)